├── .devcontainer ├── Dockerfile ├── devcontainer.json ├── library-scripts │ ├── common-debian.sh │ ├── node-debian.sh │ └── python-debian.sh └── noop.txt ├── .gitignore ├── .gitmodules ├── .pylintrc ├── LICENSE ├── README.md ├── mxfold2 ├── __init__.py ├── __main__.py ├── bpseq2fa.py ├── compbpseq.py ├── dataset.py ├── fold │ ├── embedding.py │ ├── fold.py │ ├── layers.py │ ├── mix.py │ ├── rnafold.py │ ├── transformer.py │ └── zuker.py ├── loss.py ├── models │ ├── TrainSetAB.conf │ └── TrainSetAB.pth ├── param_turner2004.py ├── predict.py ├── show_param.py ├── src │ ├── CMakeLists.txt │ ├── fold │ │ ├── fold.cpp │ │ ├── fold.h │ │ ├── nussinov.cpp │ │ ├── nussinov.h │ │ ├── trimatrix.h │ │ ├── zuker.cpp │ │ └── zuker.h │ ├── interface.cpp │ └── param │ │ ├── bpscore.cpp │ │ ├── bpscore.h │ │ ├── mix.cpp │ │ ├── mix.h │ │ ├── positional.cpp │ │ ├── positional.h │ │ ├── turner.cpp │ │ ├── turner.h │ │ └── util.h ├── train.py └── utils │ ├── avg-res.py │ ├── bpp2prob.py │ ├── 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